Development of a single-source extraction method for soil virome and microbiome analysis.

The complex interplay between microbes and viruses is a key driver of soil health and ecosystem function. However, studying these interactions is profoundly challenged by the heterogeneous nature of soil, which introduces significant bias when separate methods are used to analyze microbial and viral communities. The primary goal of this project was to develop and validate a novel, unified extraction protocol, SS-VIME (Single-Source Virome-Microbiome Extraction), to address this limitation. Our method uses a single soil sample to sequentially isolate high-quality DNA and double-stranded RNA (dsRNA) fractions. This single-source approach enables the direct, parallel profiling of bacterial and fungal communities (via DNA) and the active portion of the virome (via dsRNA), eliminating inter-extraction bias. Ultimately, this work provides a critical tool for accurately studying in situ virus-host dynamics, which are fundamental to nutrient cycling, carbon transformation, and a more holistic understanding of soil ecology.